Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery. [Display omitted] • 2D geometrical depiction of small molecules now in wwPDB ligand validation • 3D views of electron density fits for X-ray small molecules are also included • Depositor-defined research focus (LOI) highlighted in report • Carbohydrate branched representations and 2D SNFG images are introduced in the report The Worldwide Protein Data Bank (wwPDB) has enhanced validation reports generated for small-molecule ligands and carbohydrates to help ensure PDB data quality. Feng et al. describe improvements which include two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates and 3D electron density maps and difference maps for X-ray structures. [ABSTRACT FROM AUTHOR]